After a lot of trial and error and many replaced parts I have finally found the source of my driver's side foot well leak. The water is following the hood latch release cable from inside the wheel well into the cabin. Any suggestions for stopping the leak? A boat load of caulk or RTV sealant?

 

I'm not sure how water would be getting past the wheel well liner. Is it broken or damaged?

If you remove the wheel well liner, you will find a rubber grommet behind the fender. This grommet is where the hood release cable runs.

Check to see if the grommet is in tact. You are not required to remove the fender for access but this area is quite tight.

If the grommet is broken, damaged or missing you may be able to replace it. It would be a cheap part.

If the grommet is in tact, I would suspect that the leak is coming from between the seams of the body panels.
If you can see behind the fender, check to see if the factory seam sealer is in tact.

 

The Honda dealership sold it to me without wheel liners or the splash guard in the front. Something I didn't figure out until later on. I've been debating on whether it was worth replacing them but I guess this is my sign.

After jacking up the car and taking off the wheel it seems like the grommet is intact and seated properly. I will probably throw some RTV sealant on it for now to see if that helps. The water seems to be following the cable through the grommet into the cabin versus getting around the grommet.

 

without wheel well liners ? i assume we have them...thats kinda weird

I doubt the bellypan does that much..been fighting with that thing for 9 years!